The mouse t-complex on chromosome 17 has long been a focus of interest for developmental biologists. Because many embryonic lethal mutations are localized in the region, and corresponding genes of importance in development are therefore inferred to reside there, it is a prime target for high priority sequence analysis. The findings of our collaborators that the region contains a large number of otherwise unknown genes, including many expressed selectively in the ectoplacental cone, both underlines the importance of the region and provides probes to screen for substrates for long-range sequence analysis. We have thus started to map and analyze a multimegabase portion of the t- complex. From the initially targeted 10 Mb of overlapping sequenced tagged site/bacterial artificial chromosomes (BACs) physical map , the sequencing of 1.282 Mb of BAC clones has been completed with greater than 99.9% accuracy. The GC content of the sequenced region varies from 40% to a high of 50%, with a corresponding range of gene concentations.Our main tools for sequence analysis are comparison with the Genbank EST database, the exon-predicting program GRAIL, the repetitive sequence-finding program CENSOR, and the use of CpG content as an assay for CpG islands and genes. Thus far, complete annotation of one BAC 126c8 has identified 11 genes of which 5 are known genes. They are Rsp29, Als, Nubp3, Jsap1, and Ndk3. The remaining 6 predicted genes are new. Preliminary sequence analysis of the 6 additional BACs has identified genes for a fragmentary version of Rsk3, Stromelysin, Chloride channnel 7, Ubiquitin conjugating enzyme, and Pdpk1; and for a cluster of Zinc Finger-containing proteins that include ZNF54, ZFP51, and Zfp118 as well as an additional previously-undetected ZNF family member. Currently another 2 Mb of sequencing is in progress, targeting regions that include several embryonic lethal loci.